JAL-2422 tidy of methods and parameters

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index b6e6a65..3b4a958 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -379,28 +379,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
-        // TODO is performing selectioncom redundant here? is done later on
-        // System.out.println("Select regions:\n" + selectioncom.toString());
-        executeCommand("select *; cartoons off; backbone; select ("
-                + selectioncom.toString() + "); cartoons; ", false);
-        // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        // System.out.println("Superimpose command(s):\n" + cmdString);
-
         executeCommand(cmdString, false);
       }
     }
     if (selectioncom.length() > 0)
-    {// finally, mark all regions that were superposed.
-      if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+    {
+      /*
+       * finally, highlight with cartoons the residues that were superposed
+       */
+      if (selectioncom.charAt(selectioncom.length() - 1) == '|')
       {
         selectioncom.setLength(selectioncom.length() - 1);
       }
-      // System.out.println("Select regions:\n" + selectioncom.toString());
       executeCommand("select *; cartoons off; backbone; select ("
               + selectioncom.toString() + "); cartoons; ", false);
-      // evalStateCommand("select *; backbone; select "+selcom.toString()+";
-      // cartoons; center "+selcom.toString());
     }
 
     return null;

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 0192993..9695eae 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -673,18 +673,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
   }
 
-  // End StructureListener
-  // //////////////////////////
-
-  /**
-   * map between index of model filename returned from getPdbFile and the first
-   * index of models from this file in the viewer. Note - this is not trimmed -
-   * use getPdbFile to get number of unique models.
-   */
-  private int _modelFileNameMap[];
-
-  // ////////////////////////////////
-  // /StructureListener
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -941,8 +929,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   public int sendFeaturesToViewer(AlignmentViewPanel avp)
   {
     // TODO refactor as required to pull up to an interface
-    AlignmentI alignment = avp.getAlignment();
-
     String[] files = getStructureFiles();
     if (files == null)
     {

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index daf31fc..0768c00 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -28,6 +28,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
@@ -38,7 +39,6 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Rectangle;
-import java.awt.event.ActionEvent;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
@@ -404,7 +404,7 @@ public class AppJmol extends StructureViewerBase
         }
         else
         {
-          alignStructs_withAllAlignPanels();
+          alignStructsWithAllAlignPanels();
         }
       }
     });
@@ -516,41 +516,40 @@ public class AppJmol extends StructureViewerBase
   }
 
   @Override
-  public void eps_actionPerformed(ActionEvent e)
+  public void eps_actionPerformed()
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+    makePDBImage(ImageMaker.TYPE.EPS);
   }
 
   @Override
-  public void png_actionPerformed(ActionEvent e)
+  public void png_actionPerformed()
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+    makePDBImage(ImageMaker.TYPE.PNG);
   }
 
-  void makePDBImage(jalview.util.ImageMaker.TYPE type)
+  void makePDBImage(ImageMaker.TYPE type)
   {
     int width = getWidth();
     int height = getHeight();
 
-    jalview.util.ImageMaker im;
+    ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.TYPE.PNG)
+    if (type == ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+      im = new ImageMaker(this, ImageMaker.TYPE.PNG,
+              "Make PNG image from view",
               width, height, null, null, null, 0, false);
     }
-    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    else if (type == ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+      im = new ImageMaker(this, ImageMaker.TYPE.EPS,
+              "Make EPS file from view",
               width, height, null, this.getTitle(), null, 0, false);
     }
     else
     {
-
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+              ImageMaker.TYPE.SVG, "Make SVG file from PCA",
               width, height, null, this.getTitle(), null, 0, false);
     }
 
@@ -562,7 +561,7 @@ public class AppJmol extends StructureViewerBase
   }
 
   @Override
-  public void showHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed()
   {
     try
     {

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index a92fe77..22336b9 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -556,7 +556,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           @Override
           public void run()
           {
-            alignStructs_withAllAlignPanels();
+            alignStructsWithAllAlignPanels();
           }
         }).start();
       }
@@ -632,21 +632,21 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  public void eps_actionPerformed(ActionEvent e)
+  public void eps_actionPerformed()
   {
     throw new Error(MessageManager
             .getString("error.eps_generation_not_implemented"));
   }
 
   @Override
-  public void png_actionPerformed(ActionEvent e)
+  public void png_actionPerformed()
   {
     throw new Error(MessageManager
             .getString("error.png_generation_not_implemented"));
   }
 
   @Override
-  public void showHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed()
   {
     try
     {
@@ -762,9 +762,9 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @return
    */
   @Override
-  protected String alignStructs_withAllAlignPanels()
+  protected String alignStructsWithAllAlignPanels()
   {
-    String reply = super.alignStructs_withAllAlignPanels();
+    String reply = super.alignStructsWithAllAlignPanels();
     if (reply != null)
     {
       statusBar.setText("Superposition failed: " + reply);

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d3e6d75..aa39ee7 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -604,7 +604,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        viewerColour_actionPerformed(actionEvent);
+        viewerColour_actionPerformed();
       }
     });
     colourMenu.add(viewerColour);
@@ -620,7 +620,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        background_actionPerformed(actionEvent);
+        background_actionPerformed();
       }
     });
     colourMenu.add(backGround);
@@ -651,7 +651,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        seqColour_actionPerformed(actionEvent);
+        seqColour_actionPerformed();
       }
     });
 
@@ -663,7 +663,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chainColour_actionPerformed(actionEvent);
+        chainColour_actionPerformed();
       }
     });
 
@@ -675,7 +675,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chargeColour_actionPerformed(actionEvent);
+        chargeColour_actionPerformed();
       }
     });
 
@@ -707,7 +707,7 @@ public abstract class StructureViewerBase extends GStructureViewer
                 else
                 {
                   // update the Chimera display now.
-                  seqColour_actionPerformed(null);
+                  seqColour_actionPerformed();
                 }
               }
             });
@@ -757,12 +757,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    * the operation.
    */
   @Override
-  protected String alignStructs_actionPerformed(ActionEvent actionEvent)
-  {
-    return alignStructs_withAllAlignPanels();
-  }
-
-  protected String alignStructs_withAllAlignPanels()
+  protected String alignStructsWithAllAlignPanels()
   {
     if (getAlignmentPanel() == null)
     {
@@ -809,7 +804,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void background_actionPerformed(ActionEvent actionEvent)
+  public void background_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
             MessageManager.getString("label.select_background_colour"),
@@ -821,7 +816,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewerColour_actionPerformed(ActionEvent actionEvent)
+  public void viewerColour_actionPerformed()
   {
     if (viewerColour.isSelected())
     {
@@ -831,21 +826,21 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  public void chainColour_actionPerformed()
   {
     chainColour.setSelected(true);
     getBinding().colourByChain();
   }
 
   @Override
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  public void chargeColour_actionPerformed()
   {
     chargeColour.setSelected(true);
     getBinding().colourByCharge();
   }
 
   @Override
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  public void seqColour_actionPerformed()
   {
     AAStructureBindingModel binding = getBinding();
     binding.setColourBySequence(seqColour.isSelected());
@@ -873,7 +868,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  public void pdbFile_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
@@ -924,7 +919,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  public void viewMapping_actionPerformed()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
@@ -986,7 +981,7 @@ public abstract class StructureViewerBase extends GStructureViewer
 
     if (!binding.isLoadingFromArchive())
     {
-      seqColour_actionPerformed(null);
+      seqColour_actionPerformed();
     }
   }
 

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 83d8590..1fccdcb 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -104,7 +104,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        pdbFile_actionPerformed(actionEvent);
+        pdbFile_actionPerformed();
       }
     });
 
@@ -115,7 +115,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        png_actionPerformed(actionEvent);
+        png_actionPerformed();
       }
     });
 
@@ -126,7 +126,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        eps_actionPerformed(actionEvent);
+        eps_actionPerformed();
       }
     });
 
@@ -137,7 +137,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        viewMapping_actionPerformed(actionEvent);
+        viewMapping_actionPerformed();
       }
     });
 
@@ -167,7 +167,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        showHelp_actionPerformed(actionEvent);
+        showHelp_actionPerformed();
       }
     });
     alignStructs = new JMenuItem();
@@ -178,7 +178,7 @@ public abstract class GStructureViewer extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        alignStructs_actionPerformed(actionEvent);
+        alignStructsWithAllAlignPanels();
       }
     });
 
@@ -216,54 +216,53 @@ public abstract class GStructureViewer extends JInternalFrame
   {
   }
 
-  protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+  protected void viewerColour_actionPerformed()
   {
   }
 
-  protected abstract String alignStructs_actionPerformed(
-          ActionEvent actionEvent);
+  protected abstract String alignStructsWithAllAlignPanels();
 
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  public void pdbFile_actionPerformed()
   {
 
   }
 
-  public void png_actionPerformed(ActionEvent actionEvent)
+  public void png_actionPerformed()
   {
 
   }
 
-  public void eps_actionPerformed(ActionEvent actionEvent)
+  public void eps_actionPerformed()
   {
 
   }
 
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  public void viewMapping_actionPerformed()
   {
 
   }
 
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  public void seqColour_actionPerformed()
   {
 
   }
 
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  public void chainColour_actionPerformed()
   {
 
   }
 
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  public void chargeColour_actionPerformed()
   {
 
   }
 
-  public void background_actionPerformed(ActionEvent actionEvent)
+  public void background_actionPerformed()
   {
 
   }
 
-  public void showHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed()
   {
 
   }